Rev Language Reference
clade - Clade
A clade is a subtree within a phylogeny.
Usage
clade(String ..., String[] ..., Clade ..., Taxon ..., Taxon[] ..., RealPos age, String name, Natural missing, Bool negative, Bool optional_match)
Arguments
| ... : | String (pass by const reference) |
| Taxon names as string values. | |
| ... : | String[] (pass by const reference) |
| Taxon names as a vector of string values. | |
| ... : | Clade (pass by const reference) |
| Taxa as clade objects. | |
| ... : | Taxon (pass by const reference) |
| Taxon names as taxon values | |
| ... : | Taxon[] (pass by const reference) |
| Taxon names as a vector of taxons | |
| age : | RealPos (pass by value) |
| The age of the clade (optional). | |
| Default : NULL | |
| name : | String (pass by value) |
| The name of the clade (optional). | |
| Default : NULL | |
| missing : | Natural (pass by value) |
| Number of missing taxa in the clade (optional). | |
| Default : NULL | |
| negative : | Bool (pass by value) |
| Is this a negative clade constraint? | |
| Default : FALSE | |
| optional_match : | Bool (pass by value) |
| Clade constraint satisfied when any Clade argument matched | |
| Default : FALSE |
Details
Clades are defined in terms of a taxon set and a shared tree topology. In phylogenetic analyses, clades are generally used (a) to constrain tree topologies to match provided taxon relationships, (b) to identify the most recent common ancestor of a taxon set within a phylogeny, or (c) to apply node age calibrations on particular nodes in the phylogeny.
Example
# read in a tree
phy = readTrees("primates.tre")[1]
# get taxa from the tree
taxa = phy.taxa()
# create a clade for (1,2) using taxon objects
clade_12 = clade( taxa[1], taxa[2] )
# create a clade for (1,2,3)
clade_123 = clade( taxa[3], clade_12 )
# create a clade for (4,5) using taxon names
clade_45 = clade( "Taxon_4", "Taxon_5" )
# create a negative clade constraint
clade_not_23 = clade( taxa[2], taxa[3], negative=true )
# create an optional clade constraint
clade_67 = clade( taxa[6], taxa[7] )
clade_68 = clade( taxa[6], taxa[8] )
clade_67_or_68 = clade( clade_67, clade_68, optional_match=true )
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